An individual's genome provides a complete set of instructions for achieving development, regulating physiology and passing heritable information to the next generation. These instructions are encoded in the linear sequence of DNA molecules (e.g. genes) and in the higher-order structures of chromosomes and subchromosomal regions (e.g. regulatory elements). Alterations at any scale can severely impact an individual's health, survival and ability to reproduce. It is therefore not surprising that life has evolved a variety of genes and molecular pathways that contribute to maintaining the integrity of information encoded in the genome, nor is it surprising that independent evolutionary lineages have evolved novel pathways or novel modifications to their ancestral genome biology. Studying these diverse mechanisms can provide critical comparative perspective on the cellular, molecular and evolutionary underpinnings of human genome biology and have the potential to reveal new approaches to modulating related pathways in human. Following this philosophy, my lab has sought to understand the functional and evolutionary mechanisms that underlie the remarkable diversity of genome biologies that exist among deep vertebrate lineages. Our recent work has focused on dissecting the causes and consequences of programmed genome rearrangement (PGR) in the sea lamprey (Petromyzon marinus). In lampreys, PGR involves changes in the physical structure (and content) of the genome that occur in a highly predictable and programmatic manner during early development. These changes result in the reproducible loss of a specific subset of genes from all somatic cell lineages. In total, approximately 20% of the lamprey's genome is eliminated from somatic cells and retained only by germ cells. Recent progress in this line of research has shed light on the cellular/developmental mechanisms of PGR and the functions of eliminated genes. Our analyses of PGR have demonstrated that canonical silencing mechanisms (DNA and histone methylation) contribute to elimination of DNA during PGR, particularly during later stages of elimination. These studies have also revealed that eliminated genes contribute to the development/maintenance of germline when normally expressed and oncogenesis when somatically misexpressed (in other vertebrates). This proposal seeks to continue our efforts in characterizing the mechanisms and functional outcomes of PGR and extend these toward identifying genes and molecular pathways that can impact the biology of the human genome, germ/stem cells and cancer. Proposed studies aim to address several outstanding challenges with respect to PGR: 1) Precisely defining the sequence context of PGR-associated epigenetic changes and their interactions with other molecules, 2) Identifying other pathways that contribute to PGR, especially the earliest stages that involve the targeting of sequences for elimination and the differential migration of eliminated chromatin during anaphase, and 3) Characterizing the function of eliminated genes, particularly in the contexts of genome stability/instability and reprogramming. ! 1!